University of Helsinki re­search­ers de­ve­loped a se­quence analysis pipeline for virus dis­cov­ery

A novel bioinformatics pipeline identifies both previously known and novel viruses.

Researchers from the University of Helsinki have developed a novel bioinformatics pipeline called Lazypipe for identifying viruses in host-associated or environmental samples.

The pipeline was developed in close collaboration between virologists and bioinformaticians. The researchers believe they have succeeded to address many challenges typically encountered in viral metagenomics.

Previously, the Viral Zoonooses Research Unit, led by Professor Olli Vapalahti, has published two examples of novel and potentially zoonotic viral agents that were identified with Lazypipe from wild animals that can serve as vectors. A new ebolavirus was identified from faeces and organ samples of Mops condylurus bats in Kenya, and a new tick-borne pathogen Alongshan virus from ticks in Northeast Europe.

“These examples demonstrate the efficacy of Lazypipe data analysis for NGS libraries with very different DNA/RNA backgrounds, ranging from mammalian tissues to pooled and crushed arthropods,” says Dr.Teemu Smura.

Lazypipe flowchart

Lazypipe

Binaries and scripts are displayed in white, input and output files in green

Covid-19 height­ens the need to de­tect new vir­uses rap­idly

The current Coronavirus pandemic heightens the need to rapidly detect previously unknown viruses in an unbiased way.

“The detection of SARS-CoV-2 without reference genome demonstrates the utility of Lazypipe for scenarios in which novel zoonotic viral agents emerge and can be quickly detected by NGS sequencing from clinical samples,” says Dr.Ravi Kant.

In early April, the research group tested libraries of SARS-CoV-2 positive samples with Lazypipe.

“We confirmed that the pipeline detected SARS-CoV-2 in 9 out of 10 libraries with default settings and without SARS-CoV-2 reference genome,” says Dr.Ilja Pljusnin.

“Lazypipe could play a crucial role in prediction of emerging infectious diseases,” adds Assoc. Prof. Tarja Sironen.

Source – University of Helsinki

Plyusnin I, Kant R, Jääskeläinen AJ, Sironen T, Holm L, Vapalahti O, Smura T. (2020) Novel NGS Pipeline for Virus Discovery from a Wide Spectrum of Hosts and Sample Types. Virus Evolution [Epub ahead of print]. [abstract]

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